Skip to main content
Fig. 6 | Genome Biology

Fig. 6

From: Codon usage optimization in pluripotent embryonic stem cells

Fig. 6

HetADAT-dependent translation in mouse and human ESCs. a RT-qPCR confirming downregulation of ADAT2 mRNA levels in differentiated hESCs (Diff) and embryoid bodies (EB) compared to self-renewing hESCs (Self). * p < 0.05 one-way ANOVA. b Distribution of wobble inosine (A34I) levels per tRNA (> 10 reads) shown as Violin plot with median (black line) and quartiles (dotted line). c Differences of inosine levels at A34 in differentiated versus self-renewing hESC per tRNA isotype. d Light microscopic image of self-renewing (self) human embryonic stem cells (hESCs), differentiated hESCs for 5 days (5d), and embryoid bodies (EBs) after 5 and 7 days in suspension. e Quantification of protein expression using Western blotting of OCT4, ADAT2, and ADAT3 in self-renewing (grey) and differentiating (red) hESCs for 1 day. **p < 0.01 unpaired t-test. f Quantification of protein levels using Western blotting of ADAT2 and ADAT3 after differentiating hESCs into EBs for 7 days (7d). *p < 0.05; **p < 0.01 unpaired t-test. g Log2 fold change gene translation (Ribo-seq) of indicated proteins in mouse self-renewing ESCs versus ESCs differentiated by removal LIF or grown as embryoid bodies (EB). ****p < 0.0001. h Ribo-seq fold changes (diff/self) was compared with RNA-seq fold changes (diff/self). Genes with ribosome occupancy difference two-fold higher (red), two-fold lower (blue) or similar (grey) to the mRNA level difference was identified among genes rich in hetADAT-dependent nnC codons (left) and among all genes (right). The hetADAT-dependent group was significantly enriched for genes with altered (higher and lower) ribosome occupancy

Back to article page